EIF4E RNA-Seq in K562

General Information


RBP	EIF4E
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF4E-BGKcLV15-K562
ENCODE_series_ID	ENCSR173LAM
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR033XYV
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	EIF4E-BGKcLV15-33
Rep2	EIF4E-BGKcLV15-34
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	68.1
Rep2_qPCR	50.2
Rep1_WB	95.6
Rep2_WB	94.5
Antibody Cat#	MA1-089
Antibody Lot#	LOT# TD257774
Antibody DCC ID	ENCAB864VOP
Status	Released
Project	ENCODE4
ID	127

Experiment Information (Status: Released)

	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-34	BGKcLV15-34	BGKcLV15-34
idx	569	571	571	570	572	572
TRCN#_or_BGC#	BGC#0000390	BGC#0000390	BGC#0000390	BGC#0000390	BGC#0000390	BGC#0000390
shRNA_or_gRNA_sequence	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG
PAM	GGG	GGG	GGG	GGG	GGG	GGG
Name	EIF4E_80	EIF4E_80	EIF4E_80	EIF4E_80	EIF4E_80	EIF4E_80
Sample_ID	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-34	BGKcLV15-34	BGKcLV15-34
transduction_Date	4/2/19	4/2/19	4/2/19	4/2/19	4/2/19	4/2/19
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	EIF4E	EIF4E	EIF4E	EIF4E	EIF4E	EIF4E
qPCR_result	68.1	68.1	68.1	50.2	50.2	50.2
Ave_qPCR	59.2	59.2	59.2
RT-qPCR_primer-F	AGAAAAACAAACGGGGAGGA	AGAAAAACAAACGGGGAGGA	AGAAAAACAAACGGGGAGGA
RT-qPCR_primer-R	TCAAAAGATTCTCCAATAAGGCA	TCAAAAGATTCTCCAATAAGGCA	TCAAAAGATTCTCCAATAAGGCA
protein_conc	5166	5166	5166	5479	5479	5479
WB_result	95.6	71.2	77.7	94.5	67.3	77.6218
Ave_WB	95.1	69.3
WB_DONE_date	4/9/19	5/7/19	11/15/24
MW	25KD	25KD	25KD
IP	Mouse / Ig	Rabbit / I			EIF4E pSer
antibody_Cat#	MA1-089	44-528G	2067S	LOT# TD257774	LOT# SG256167	LOT# 8
Antibody DCC ID	ENCAB864VOP	ENCAB617EPT
submitted_to_DCC_date	4/17/19	4/17/19
Rep1_TPM	116.7	116.7	0	0	0	0
Rep2_TPM	130.1	130.1	0	0	0	0
Action	Ready			Ready
Library_start_date	05/30/19			05/30/19
repeat_library
Note
ID	4679	4681	4683	4680	4682	4684

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4E	Product_ID: MA1-089 Lot_ID: TD257774 Source: Thermo Fisher Target Name: EIF4E-human
EIF4E	Product_ID: 44-528G Lot_ID: SG256167 Source: Thermo Fisher Target Name: EIF4EphosphoS209-human Phosphate: pSer209
EIF4E	Product_ID: 2067S Lot_ID: 8 Source: Cell Signaling Technology Target Name: EIF4E-human

Experiment Status

	BGKcLV15-33	BGKcLV15-34
Sample_ID	BGKcLV15-33	BGKcLV15-34
Sample Name
Sample Name	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-34
RBP	EIF4E	EIF4E
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5343	5344

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-33	BGKcLV15-34
Sample #	13	14
Sample Name	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-34
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	1-E2	1-F2
Tecan	34.34	38.24
Tecan_date	2019-12-10	2019-12-10
Size_bp	270	268
Peak_Molarity	20.70	23.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E2.png	DNA_Library_set43-44/set1/F2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/E2.png	RNA_Library_set43-44/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-33	BGKcLV15-34
RBP	EIF4E	EIF4E
Batch_ID	BGKcLV15	BGKcLV15
WB_result	95.600	94.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	589	590

Sequencing Information

	BGKcLV15-33	BGKcLV15-34
Sample_ID	BGKcLV15-33	BGKcLV15-34
Sample Name	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-34
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	98,620,334	105,509,982
total_aligned_reads	83,539,300	94,967,792
unique_aligned_reads	76,078,060	86,420,920
percent_uniqueAligned	0.77142	0.81908
correlation_replicates	0.999619	0.999619
spikein_reads	59,516	71,800
percent_spikeins	0.00060	0.00068
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	95	96

Data Submission Information

	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-34	BGKcLV15-34	BGKcLV15-34	BGKcLV15-34
ENCODE_alias	brenton-graveley:EIF4E-BGKcLV15	brenton-graveley:EIF4E-BGKcLV15-33	brenton-graveley:L-EIF4E-BGKcLV15-33	brenton-graveley:EIF4E-BGKcLV15-33_S13_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4E-BGKcLV15-33_S13_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4E-BGKcLV15-K562	brenton-graveley:EIF4E-BGKcLV15-34	brenton-graveley:L-EIF4E-BGKcLV15-34	brenton-graveley:EIF4E-BGKcLV15-34_S14_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4E-BGKcLV15-34_S14_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR033XYV	ENCBS104TZP	ENCLB692XMT	ENCFF177VDP	ENCFF646ZHX	ENCSR173LAM	ENCBS485INP	ENCLB255NPQ	ENCFF165IOZ	ENCFF227XMS
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-33	BGKcLV15-34	BGKcLV15-34	BGKcLV15-34	BGKcLV15-34
Sample Name	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-33	EIF4E-BGKcLV15-34	EIF4E-BGKcLV15-34	EIF4E-BGKcLV15-34	EIF4E-BGKcLV15-34
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		EIF4E-BGKcLV15-33.pdf	L-EIF4E-BGKcLV15-33.pdf				EIF4E-BGKcLV15-34.pdf	L-EIF4E-BGKcLV15-34.pdf
ID	23	128	292	490	542	7204	129	293	491	543

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
EIF4E-BGKcLV15-33_S13_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	95	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	87
EIF4E-BGKcLV15-33_S13_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	95	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	139
EIF4E-BGKcLV15-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	95					GRCh38	V40	EIF4E-BGKcLV15-33_S13_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGKcLV15-33_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24378
EIF4E-BGKcLV15-33_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	95					GRCh38	V40	EIF4E-BGKcLV15-33/Aligned.sortedByCoord.out.bam		ENCORE2	24430
EIF4E-BGKcLV15-33_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	95					GRCh38	V40	EIF4E-BGKcLV15-33/Aligned.sortedByCoord.out.bam		ENCORE2	24482
EIF4E-BGKcLV15-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	95					GRCh38	V40	EIF4E-BGKcLV15-33/Aligned.sortedByCoord.out.bam		ENCORE2	24534
EIF4E-BGKcLV15-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	95					GRCh38	V40	EIF4E-BGKcLV15-33/Aligned.sortedByCoord.out.bam		ENCORE2	24586
EIF4E-BGKcLV15-33_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	95					GRCh38	V40	EIF4E-BGKcLV15-33_S13_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGKcLV15-33_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24638
EIF4E-BGKcLV15-34_S14_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	96	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	88
EIF4E-BGKcLV15-34_S14_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	96	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	140
EIF4E-BGKcLV15-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	96					GRCh38	V40	EIF4E-BGKcLV15-34_S14_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGKcLV15-34_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24379
EIF4E-BGKcLV15-34_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	96					GRCh38	V40	EIF4E-BGKcLV15-34/Aligned.sortedByCoord.out.bam		ENCORE2	24431
EIF4E-BGKcLV15-34_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	96					GRCh38	V40	EIF4E-BGKcLV15-34/Aligned.sortedByCoord.out.bam		ENCORE2	24483
EIF4E-BGKcLV15-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	96					GRCh38	V40	EIF4E-BGKcLV15-34/Aligned.sortedByCoord.out.bam		ENCORE2	24535
EIF4E-BGKcLV15-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	96					GRCh38	V40	EIF4E-BGKcLV15-34/Aligned.sortedByCoord.out.bam		ENCORE2	24587
EIF4E-BGKcLV15-34_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	96					GRCh38	V40	EIF4E-BGKcLV15-34_S14_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGKcLV15-34_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24639